But Hercules and Wonder Man (the non-pacifist non-weird version) could do the buddy thing like Wonder Man and the Beast did. And we can't have a Wonder Man and the Beast movie because Marvel can't use their own character - the blue furry one.

I would keep Wonder Man earthbound. No flying. Only because (a) Hercules can't fly so I wouldn't want Wonder Man flying either and (b) flying actually simplifies situations for the hero in boring ways. Neither Spider-Man, nor Wolverine, nor Batman can fly - and they're the three most popular super-heroes.

I wouldn't use ionic Wonder Man. I hate the ionic thing.

Hercules's origin is easy, he's the actual Greek demigod. Spend five minutes on it and move on. As for Wonder Man, I would start him out as a pawn of Hercules's enemy Ares. (This harkens back to the actual Wonder Man origin, as he started out as a pawn of an Avengers enemy.) Ares would give Simon Williams super strength and construct some scheme for Wonder Man to carry out, so as to trick Hercules into becoming vulnerable in some way. But when it becomes apparent that Ares is about to kill Hercules, Wonder Man relents and attacks Ares. Hercules forgives Wonder Man and they become buddies. Wonder Man doesn't die. I think this captures the spirit of Wonder Man's comic book origin and hits the important emotional elements. Except for the dying. We can't have the dying. Also we don't need his brain patterns for the Vision in the film universe.

These two guys then have an adventure in classic buddy film style. The new villain would be the Grim Reaper, Simon's brother. Thus we get a Hercules rogue and a Wonder Man rogue in the same film.